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Plant hydraulic characteristics were studied in diploid, tetraploid and hexaploid cytotypes of Atriplex canescens (Chenopodiaceae) to investigate the potential physiological basis underlying the intraspecific habitat differentiation among plants of different ploidy levels. Populations of A. canescens from different habitats of the Chihuahuan Desert (New Mexico, USA) were analyzed using flow cytometry to determine ploidy levels. Traits related to xylem water transport efficiency and safety against drought-induced hydraulic failure were measured in both stems and leaves. At the stem level, cytotypes of higher ploidy showed consistently lower leaf-specific hydraulic conductivity but greater resistance to drought-induced loss of hydraulic conductivity. At the leaf level, comparisons in hydraulics between cytotypes did not show a consistent pattern, but exhibited high plasticity to proximal environmental conditions related to soil water availability. The results suggest that a trade-off between stem hydraulic efficiency and safety across ploidy levels underlies niche differentiation among different cytotypes of A. canescens. Polyploidization may have been facilitated by environmental heterogeneity related to water availability, and variation in water-related physiology found in the present study suggests an important functional basis for the niche differentiation and coexistence of A. canescens cytotypes in desert environments.